def test_reorient(self):
"""Test the reorient command of the CLI"""
# Reorienting the streamlines should do nothing (they are already)
# correctly oriented.
output = os.path.join(self.test_dir.name, 'test-reorient-1.trk')
reorient(
os.path.join(self.test_dir.name, 'bundle.trk'),
output)
streamlines = load(os.path.join(self.test_dir.name, 'bundle.trk'))
new_streamlines = load(output)
for streamline, new_streamline in zip(streamlines, new_streamlines):
np.testing.assert_array_almost_equal(new_streamline._points,
streamline._points)
# Reorienting the bundle with the reversed first streamline
# should reverse every streamline.
output = os.path.join(self.test_dir.name, 'test-reorient-2.trk')
reorient(
os.path.join(self.test_dir.name, 'bundle-flipped.trk'),
output)
streamlines = load(os.path.join(self.test_dir.name, 'bundle.trk'))
new_streamlines = load(output)
for streamline, new_streamline in zip(streamlines, new_streamlines):
np.testing.assert_array_almost_equal(new_streamline._points,
streamline._points)
def view(filename):
"""View streamlines in interactive window"""
# Load the streamlines to be displayed.
streamlines = load(filename)
# Create a new vtk renderer and rendering window.
renderer = vtk.vtkRenderer()
renderer.SetViewport(0.0, 0.0, 1.0, 1.0)
renderer.SetBackground(0.0, 0.0, 0.0)
rendering_window = vtk.vtkRenderWindow()
rendering_window.AddRenderer(renderer)
# Allow the user to interact with the mesh.
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(rendering_window)
interactor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
# Compute the number of points.
nb_points = 0
for streamline in streamlines:
nb_points += len(streamline)
# The vtk points and lines that represent the lines to draw.
points = vtk.vtkPoints()
points.SetNumberOfPoints(nb_points)
lines = vtk.vtkCellArray()
# Copy the point and streamline data to vtk objects.
point_count = 0
for streamline in streamlines:
lines.InsertNextCell(len(streamline))
for idx, point in enumerate(streamline):
points.SetPoint(point_count, point[0], point[1], point[2])
lines.InsertCellPoint(point_count)
point_count += 1
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(points)
poly_data.SetLines(lines)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(poly_data)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetOpacity(0.01)
actor.GetProperty().SetLineWidth(1)
# Add the actor to the renderer.
renderer.AddActor(actor)
# Start rendering.
rendering_window.Render()
interactor.Start()
# Cleanup when the user closes the window.
rendering_window.Finalize()
interactor.TerminateApp()
def filter(input, output, **kwargs):
# Load the input streamlines using the requested parameters.
streamlines = load(input)
streamlines.filter(**kwargs)
# Save the streamlines to the output file.
save(streamlines, output)
def merge(inputs, output):
# Load all the input streamlines and merge them.
streamlines_list = [load(i) for i in inputs]
streamlines = reduce(operator.iadd, streamlines_list)
# Save the streamlines to the output file.
save(streamlines, output)
def test_merge(self):
"""Test the merge command of the CLI"""
# Merging the short and random streamlines should yield a tractogram
# with 4 streamlines.
inputs = [os.path.join(self.test_dir.name, i)
for i in ['short.trk', 'random.trk']]
output = os.path.join(self.test_dir.name, 'test-merge-1.trk')
merge(inputs, output)
streamlines = load(output)
self.assertEqual(len(streamlines), 4)
# Merging the shord and empty files should yield 3 streamlines.
inputs = [os.path.join(self.test_dir.name, i)
for i in ['short.trk', 'empty.trk']]
output = os.path.join(self.test_dir.name, 'test-merge-2.trk')
merge(inputs, output)
streamlines = load(output)
self.assertEqual(len(streamlines), 3)
def test_filter(self):
"""Test the filter command of the CLI"""
# Filter the short streamlines. The result should be an empty tractogram.
output = os.path.join(self.test_dir.name, 'test-filter-1.trk')
filter(
os.path.join(self.test_dir.name, 'short.trk'),
output,
min_length=1.1)
streamlines = load(output)
self.assertEqual(len(streamlines), 0)
def info(input):
# Load the input streamlines using the requested parameters.
streamlines = load(input)
# Print info about the streamlines.
out = ''
out += '\nNumber of streamlines: {}'.format(len(streamlines))
out += '\nMean length: {:.2f}'.format(np.mean(streamlines.lengths))
print(out)
def filter(input_filename, output_filename, **kwargs):
"""Removes streamlines from a file based on features
Removes streamlines from a file based on their features. For example,
remove all streamlines with a length below 50mm using --min-length 50.
Args:
input_filename: The file that contains the streamlines to filter.
output_filename: The file where the remaining streamlines will be
saved.
"""
# Load the input_streamlines using the requested parameters.
streamlines = load(input_filename)
streamlines.filter(**kwargs)
# Save the streamlines to the output file.
save(streamlines, output_filename)
def smooth(input_filename, output_filename, **kwargs):
"""Smooths streamlines in a file
Smooths streamlines using a least square b-spline. The distance between
knots controls the smoothness of the output streamline with larger
distances being smoother
Args:
input_filename: The file that contains the streamlines to smooth.
output_filename: The file where the smoothed streamlines will be saved.
"""
# Load the input streamlines using the requested parameters.
streamlines = load(input_filename)
streamlines.smooth(**kwargs)
# Save the streamlines to the output file.
save(streamlines, output_filename)
def info(streamlines_filename):
"""Print information about a streamlines file
Prints the number of streamlines in the file and the mean length of the
streamlines.
Args:
streamlines_filename: The file whose info is printed.
"""
# Load the input streamlines using the requested parameters.
streamlines = load(streamlines_filename)
# Print info about the streamlines.
out = ''
out += '\nNumber of streamlines: {}'.format(len(streamlines))
out += '\nMean length: {:.2f}'.format(np.mean(streamlines.lengths))
print(out)
def transform(input, output):
"""Transforms streamlines from one fileformat to another"""
streamlines = load(input)
save(streamlines, output)
